[Chimera-users] Structural alignment of a protein-ligand complex with other ligands only

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 9 09:10:37 PDT 2010

Here is an explanation of the different ways to superimpose structures in Chimera, to help you decide which one to use in your situation:

Follow the links if you want to see more details about any of the methods.

You are right that MatchMaker pairs up protein chains or nucleotide chains, but the structures can contain additional parts -- you don't have to use them all for fitting. If two structures share a similar protein chain or a similar DNA chain, you could use just that chain in MatchMaker to superimpose them (the rest of the structure would come along).  Or, if you want to use a specific list of atoms instead (for example, ligands or parts of ligands) you could do that with the "match" command. 

The URL above is in the User's Guide on our web site, but you also have a complete copy of the User's Guide included with your Chimera download.  You can access it from the Help menu in Chimera.  For example, you would see the equivalent page by choosing "Help... User's Guide" from the menu, then going to the "Basic Functions" section, then clicking "Superimposing Structures" (#16 or thereabouts in the basic functions index).

The User's Guide includes tutorials with examples of superimposing structures, and is also keyword-searchable from the Help menu in Chimera (Help... Search Documentation). 
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 8, 2010, at 10:35 PM, N.R. Jena wrote:

> Hi,
> We are new to Chimera. Can you please let us know, if we have to
> superpose a protein-ligand complex with other ligands or a DNA-protein
> complex with few nucleotide-peptide complex, what is the better way to
> do in Chimera. I guess MatchMaker option is meant for superposition of
> one DNA or Protein on another DNA or Protein, right?

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